We propose to develop computational methods and software to systematically identify and comprehensively verify conserved cis-regulatory modules (CRMs) located in the non-coding regions of the human genome. These conserved CRMs include those in the well aligned regions in the orthologous sequence alignments as well as those in the shuffled regions of the genome. To our knowledge, there is no existing computational method targeting to identify the latter at a whole genome level, although these shuffled conserved CRMs are frequently present in vertebrate genomes. Specifically, we have the following aims: 1. Develop computational methods to systematically identify conserved CRMs on the whole genome scale. 2. Integrate multiple sources of information to judge whether identified CRMs are bona fide CRMs and to predict the possible functions of the CRMs. Experimentally validate the function of up to 600 CRMs in the ENCODE regions. 3. Develop user-friendly software to support studies of gene regulation in the human genome. This project will significantly enhance our understanding of the global transcriptional regulation in the human genome. The conserved CRMs in vertebrate provide a rich resource for better understanding of the occurrence of many congenital diseases. The predicted CRMs and their putative functions will benefit the development of the therapeutic approaches to attack many serious diseases, such as lung and breast cancer, cardiovascular disease, infectious diseases, which are caused by dysfunction of CRMs under certain conditions.